30 - Bernstein, J. G., Boyden, E. S. (2011) Optogenetic tools for analyzing the neural circuits of behavior, in press, Trends in Cognitive Sciences. doi:10.1016/j.tics.2011.10.003

29 - Kleinlogel, S., Terpitz, U., Legrum, B., Gokbuget, D., Boyden, E. S., Bamann, C., Wood, P. G., Bamberg, E. (2011) A gene- fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins, Nature Methods, advance online publication. doi:10.1038/nmeth.1766

28 - Bernstein, J. G., Garrity, P. A.*, Boyden, E. S.* (2011) Optogenetics and thermogenetics: technologies for controlling the activity of targeted cells within intact neural circuits, Current Opinion in Neurobiology, in press, doi:10.1016/j.conb.2011.10.023. (* co-corresponding authors)

27 - Kahn, I. * Desai, M., Knoblich, U., Bernstein, J., Henninger, M., Graybiel, A. M., Boyden, E. S.*, Buckner, R. L. *, Moore, C. I. * (2011) Characterization of the Functional MRI Response Temporal Linearity via Optical Control of Neocortical Pyramidal Neurons, Journal of Neuroscience 31(42):15086-15091. (* co-corresponding authors)

26 - Tsunematsu, T., Kilduff, T., Boyden, E. S., Takahashi, S., Tominaga, M., Yamanaka, A. (2011) Acute optogenetic silencing of orexin/hypocretin neurons induces slow wave sleep in mice, Journal of Neuroscience, 31(29): 10529-10539.

25 - Joo, J., Chow, B. Y., Prakash, M., Boyden, E. S., Jacobson, J. M. (2011) Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis, Nature Materials, 10(8):596-601.

24 - Wentz, C. T., Bernstein, J. G., Monahan, P., Guerra, A., Rodriguez, A., Boyden, E. S. (2011) A Wirelessly Powered and Controlled Device for Optical Neural Control of Freely-Behaving Animals, Journal of Neural Engineering 8(4): 046021 doi: 10.1088/1741-2560/8/4/046021

23 - Chow, B. Y. and Boyden, E. S. (2011) Synthetic Physiology, Science 332(6037):1508-1509.

22 - McCarthy, M. M., Moore-Kochlacs, C., Xuan Gu, T., Boyden, E. S., Han, X., Kopell, N. J. (2011) Striatal origin of the pathologic beta oscillations in Parkinson’s disease, Proceedings of the National Academy of Sciences, 108(28):11620-5.

21 - Chow, B. Y., Chuong, A. S., Klapoetke, N. C., Boyden, E. S. (2011) Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes, Chapter 18, Methods in Enzymology: Synthetic Biology, Part A: Methods for Part/Device Characterization and Chassis Engineering, edited by Christopher Voigt, Volume 497, Elsevier.

20 - Boyden, E. S. (2011) A history of optogenetics: the development of tools for controlling brain circuits with light. F1000 Biology Reports, 3:11 (doi:10.3410/B3-11)

19 - Doroudchi, M. M., Greenberg, K. P., Liu, J., Silka, K. A., Boyden, E. S., Lockridge, J. A., Arman, A. C., Janani, R., Boye, S. E., Boye, S. L., Gordon, G. M., Matteo, B. C., Sampath, A. P., Hauswirth, W. W., Horsager, A. (2011) Virally delivered Channelrhodopsin-2 Safely and Effectively Restores Visual Function in Multiple Mouse Models of Blindness, Molecular Therapy, 19(7):1220-9

18 - Han, X.*, Chow, B. Y.*, Zhou, H., Klapoetke, N. C., Chuong, A., Rajimehr, R., Yang, A., Baratta, M. V., Winkle, J., Desimone, R., Boyden, E. S. (2011) A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Frontiers in Systems Neuroscience. 5:18. doi: 10.3389/fnsys.2011.00018 (* co-first authors)

17 - Desai M., Kahn I., Knoblich U., Bernstein J., Atallah H., Yang A., Kopell, N., Buckner R.L., Graybiel A. M., Moore C. I.*, and Boyden E. S.* (2011) Mapping Brain Networks in Awake Mice Using Combined Optical Neural Control and fMRI, Journal of Neurophysiology 105(3):1393-405. (* co-corresponding authors)

16 - Zorzos, A. N., Boyden, E. S.*, and Fonstad, C. G. (2010) Multiwaveguide implantable probe for light delivery to sets of distributed brain targets, Optics Letters 35(24):4133-5. (* corresponding author).

15 - Knopfel, T., Lin, M. Z., Levskaya, A., Tian, L., Lin, J. Y., Boyden, E. S. (2010) Toward the Second Generation of Optogenetic Tools, Journal of Neuroscience 30(45):14998-15004.

14 - Chan S. Y., Bernstein J. G., Boyden E. S. (2010). Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits. JoVE. 35. http://www.jove.com/index/details.stp?id=1489, doi: 10.3791/1489

13 - Chow, B. Y.*, Han, X.*, Dobry, A. S., Qian, X., Chuong, A. S., Li, M., Henninger, M. A., Belfort, G. M., Lin, Y., Monahan, P. E., Boyden, E. S. (2010) High-performance genetically targetable optical neural silencing by light- driven proton pumps, Nature 463:98-102. (* co-first authors)

12 - Han X, Qian X, Stern P, Chuong A and Boyden ES (2009) Informational Lesions: Optical Perturbation of Spike Timing and Neural Synchrony Via Microbial Opsin Gene Fusions, Frontiers in Molecular Neuroscience, 2:12. doi:10.3389/neuro.02.012.2009

11 - Han, X.*, Qian, X., Bernstein, J.G., Zhou, H.-H., Talei Franzesi, G., Stern, P., Bronson, R.T., Graybiel, A.M., Desimone, R., and Boyden, E.S.* (2009) Millisecond-Timescale Optical Control of Neural Dynamics in the Nonhuman Primate Brain, Neuron 62(2): 191-198. (* co-corresponding authors)

10 - Liao, Y. J., Safa, P., Chen, Y.-R., Sobel, R. A., Boyden, E. S., Tsien, R. W. (2008) Anti-Ca2+ channel antibody attenuates Ca2+ currents and mimics cerebellar ataxia in vivo, Proceedings of the National Academy of Sciences 105(7):2705-2710.

9 - Wang, H., Peca, J., Matsusaki, M., Matsusaki, K., Noguchi, J., Qiu, L., Wang, D., Zhang, F., Boyden, E. S., Deisseroth, K., Kasai, H., Hall, W. C., Feng, G., Augustine, G. J. (2007) High-speed mapping of synaptic connectivity using photostimulation in channelrhodopsin-2 transgenic mice, Proceedings of the National Academy of Sciences 104(19):8143-848.

8 - Han, X. and Boyden, E. S. (2007) Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution, PLoS ONE 2(3): p. e299.

7 - Zhang, F., Wang, L.-P., Boyden, E. S., Deisseroth, K. (2006) Optical control of excitable cells and Channelrhodopsin-2, Nature Methods 3(10):785-92.

6 - Boyden, E. S., Katoh, A., Pyle, J. L., Chatila, T. A., Tsien, R. W., Raymond, J. L. (2006) Selective engagement of plasticity mechanisms for motor memory storage, Neuron 51(6):823-834.

5 - Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., Deisseroth, K. (2005) Millisecond-timescale, genetically-targeted optical control of neural activity, Nature Neuroscience 8(9):1263-1268.

4 - Kimpo, R. R.*, Boyden, E. S.*, Katoh, A., Ke, M. C., Raymond, J. L. (2005) Distinct patterns of stimulus generalization of increases and decreases in VOR gain, Journal of Neurophysiology 94(5):3092-3100. (* co-first authors)

3 - Boyden, E. S.*, Katoh, A.*, Raymond, J. L. (2004) Cerebellum-dependent learning: The role of multiple plasticity mechanisms, Annual Review of Neuroscience 27:581-609. (* co-first authors)

2 - Boyden, E. S., Raymond, J. L. (2003) Active reversal of motor memories reveals rules governing memory encoding, Neuron 39(6):1031-42.

1 - Maguire, Y., Boyden, E. S., Gershenfeld, N. (2000) Toward a table-top quantum computer, IBM Systems Journal 39:3&4, p.823.

11 - Kodandaramaiah, S., Krijnen, M., Go, J., Malik, S., Sondej, N., Khatait, J. P., Boyden, E. S., Aarts, R. G. K. M., Brouwer, D. M., Forest, C. F. (2011) Characterization of translation of fused silica micropipettes in non-rectilinear trajectories, Proceedings of the 26th Annual Meeting of the American Society for Precision Engineering, Denver, CO.

10 - Doroudchi, M. M., Greenberg, K. P., Zorzos, A. N., Hauswirth, W. W., Fonstad, C. G., Horsager, A., Boyden, E. S. (2011) Towards Optogenetic Sensory Replacement, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC ’11).

9 - Boyden, E. S. (2011) Optogenetics. 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC ’11).

8 - Chow B, Han X, Qian X and Boyden E (2009). High-performance halorhodopsin variants for improved genetically-targetable optical neural silencing. Frontiers in Systems Neuroscience. Conference Abstract: Computational and systems neuroscience. doi: 10.3389/conf.neuro.10.2009.03.347

7 - Boyden E, Franzesi G T, Qian X, Li M, Han X, Borgers C, Kopell N J, Le Beau F and Whittington M A (2009). Probing mechanisms of gamma rhythmogenesis with cell type-specific optical neural control. Frontiers in Systems Neuroscience. Conference Abstract: Computational and systems neuroscience. doi: 10.3389/conf.neuro.10.2009.03.299

6 - Bernstein, J. G., Han, X., Henninger, M. A., Ko, E. Y., Qian, X., Franzesi, G. T., McConnell, J. P., Stern, P., Desimone, R., and Boyden, E. S. (2008) Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons. Proc Soc Photo Opt Instrum Eng, 6854:68540H.

5 - Han, X., and Boyden, E. S. (2007) Two-color, bi-directional optical voltage control of genetically-targeted neurons, Spotlight Presentation, at Computational and Systems Neuroscience (CoSyNe), Salt Lake City, UT, Feb 22-25, 2007.

4 - Boyden, E. S., Chatila, T. A., Raymond, J. L. (2004) The contribution of inverse plasticity mechanisms to cerebellum-dependent learning, Talk, at Computational and Systems Neuroscience (CoSyNe), Cold Spring Harbor, NY, March 24-28, 2004.

3 - Boyden, E. S., Tsien, R. W., Chatila, T. A., Raymond, J. L. (2003) Is oppositely directed motor learning implemented with inverse plasticity mechanisms?, Proceedings of the Annual Symposium on Advances in Computational Motor Control, Volume 2, Emanuel Todorov and Reza Shadmehr, editors, New Orleans, Louisiana.

2 - Fletcher, R., Omojola, O., Boyden, E. S., Gershenfeld, N. (1999) Reconfigurable Agile Tag Reader Technologies for Combined EAS and RFID capability, Proceedings of the Second IEEE Workshop on Automatic Identification Advanced Technologies, Summit, New Jersey.

1 - Schoner, B., Cooper, C., Douglas, C. L., Boyden, E. S., Gershenfeld, N. A. (1999) Data-driven modeling of acoustical instruments, Journal of the Acoustic Society of America 105(2):1328.

19 - Boyden, E. S. (2011) Enhancing the Brain - Past, Present and Future, Honors Colloquium, University of Rhode Island.

18 - Boyden, E.S. (2011) Neural Networks for Solving Neural Networks, Networks Solving Networks Meeting, MIT Media Lab, Cambridge, MA.

17 - Boyden, E. S. (2011) Controlling brain circuits with light: Towards systematic analysis of neural circuit functions. Symposium on the Emerging Genetics and Neurobiology of Severe Mental Illness, Broad Institute, Cambridge, MA.

16 - Boyden, E. S. (2011) Technologies for the Systematic Analysis of How Brain Circuits Perform Computations, Keynote, 4th Conference on Artificial General Intelligence, Google, Mountain View, CA.

15 - MIT McGovern Institute Video (2011) Optogenetics: Controlling the brain with light. Online.

14 - Boyden, E. S. (2011) A light switch for neurons. TED, Long Beach, CA.

13 - Interview. (2011) Ed Boyden: SPIE Newsroom Interview, San Francisco, CA.

12 - MIT McGovern Institute Video (2011) Blind Mice, No Longer: Video Press Release for Doroudchi et al., 2011.

11 - Boyden, E. S. (2011) Controlling the Brain With Light, SPIE, Hot Topics Session, San Francisco, CA.

10 - Boyden, E. S. (2010) Controlling Brain Computations: Towards New Brain Insights and Brain Therapies, Allen Institute for Brain Science Symposium, Open Questions in Neuroscience, Seattle, WA.

9 - Boyden, E. S. (2010) Controlling Brain Circuits With Light, EmTech@MIT, Cambridge, MA.

8 - Boyden, E. S. (2010) Enabling Systematic Neuroscience with Novel Optical Neural Control Strategies, INCF Neuroinformatics Congress, Kobe, Japan.

7 - Interview. (2010) Ed Boyden: National Science Foundation interview. Online.

6 - McGovern Institute, MIT. (2010) Welcome to the McGovern Institute. Online.

5 - Boyden, E. S. (2009) Synthetic Neurobiology: Optically Engineering the Brain to Augment Its Function, Singularity Summit, New York City, NY.

4 - Boyden, E. S. (2009) Optical Neural Control Prosthetics, Invited speaker, No Barriers Festival, Miami, FL.

3 - Boyden, E. S. (2009) Optical Control Of Normal and Pathological Neural Circuit Computations, Invited speaker, McGovern Symposium, Tsinghua University, Beijing, China.

2 - Boyden, E. S. (2009) Optical Brain Control: Analyzing and Engineering Normal and Pathological Neural Circuit Dynamics, Invited speaker, CIMIT Forum, Boston, MA.

1 - Boyden, E. S. (2007) Engineering the Brain: Towards Systematic Cures for Neural Disorders, Featured speaker, MIT Media Lab H2.0 (Human 2.0) Symposium, MIT, Cambridge, MA.

4 - Synthetic Neurobiology Memo #4 (2009) Very Simple Off-The-Shelf Laser and Viral Injector Systems for In Vivo Optical Neuromodulation. Online.

3 - Synthetic Neurobiology Memo #3 (2009) Circuit Boards and Software for Heart Rate and Galvanic Skin Response Measurements. Online.

2 - Synthetic Neurobiology Memo #2 (2009) Lentivirus production for high-titer, cell-specific, in vivo neural labeling. Online.

1 - Synthetic Neurobiology Memo #1 (2006) Versatile, but Manually-Assembled, Optical Fiber/Laser System for In Vivo (Multicolor) Light Delivery for Brain Neuromodulation. Online.

1 - List of invited talks, in reverse chronological order, with links to content (highlighted in bold text) when available.

1 - List of conference papers and talks (non-refereed), in reverse chronological order, with links to content when available.

3 - Chow, B. Y., Han, X., Bernstein, J. G., Monahan, P. E., Boyden, E. S. (2011) Light-Activated Ion Pumps and Channels for Temporally Precise Optical Control of Activity in Genetically Targeted Neurons, Chapter 6, Photosensitive Molecules for Controlling Biological Function, edited by James J. Chambers and Richard H. Kramer, Neuromethods Series Volume 55, 2011, DOI: 10.1007/978-1-61779-031-7, Humana Press.

2 - Boyden, E. S., Han, X., Talei Franzesi, G., Chan, S., Bernstein, J., Qian, X., Li, M. (2009) "New Techniques for Investigating Brain Rhythms: Optical Neural Control and Multielectrode Recording," In: Rhythms of the Neocortex: Where Do They Come From and What Are They Good For? (Kopell N., ed.) pp. 65-75. Washington, DC: Society for Neuroscience.

1 - Task Group Summary 6 (The Brain), The National Academies Keck Futures Initiative: Complex Systems: Task Group Summaries, 2009, ISBN 0-309-13725-X, National Academies Keck Future Initiative, National Academies Press, Washington DC.

12 - Methods and Apparatus for Microstructure Lightguides. United States Patent Application 12/843,587.

11 - Light-activated proton pumps and uses thereof. United States Patent Application 12/714,436.

10 - Light-Proof Electrodes. United States Patent Application 12/824,805.

9 - Scalable Parallel Gene Therapy Injector Array. United States Patent Application 12/619,685.

8 - Prosthetic system for therapeutic optical activation and silencing of genetically-targeted neurons. United States Patent Application 12/355,745.

7 - Integrated Transcranial Current Stimulation and Electroencephalography Device. United States Patent Application 12/118,092.

6 - Portable, Modular Transcranial Magnetic Stimulation Device. United States Patent Application 12/117,896.

5 - Optical Cell Control Prosthetics. United States Patent Application 12/118,673.

4 - SYSTEM FOR OPTICAL STIMULATION OF TARGET CELLS. United States Patent Application 12/522,520.

3 - LIGHT-ACTIVATED CATION CHANNEL AND USES THEREOF. United States Patent Application 11/459,636.

2 - LIGHT-ACTIVATED CATION CHANNEL AND USES THEREOF. United States Patent Application 11/459,637.

1 - LIGHT-ACTIVATED CATION CHANNEL AND USES THEREOF. United States Patent Application 11/459,638.

18 - Boyden, E. S. (2011) Optogenetics: Using Light to Control the Brain, Cerebrum, The Dana Foundation, November 2011.

17 - Boyden, E. S. (2011) The Birth of Optogenetics, The Scientist, July 2011 Issue. (Cover Story.)

16 - Boyden, E. S. (2010) "Molecular Tools for Controlling Brain Circuits with Light," Eppendorf and Science Prize for Neurobiology Competition Essay, Science Magazine.

15 - Boyden, E. S., Allen, B. D., Fritz, D. (2010) "Brain Coprocessors." Column, Technology Review. 9/23/2010.

14 - Boyden, E. S. (2010) Controlling the Brain with Light. SPIE Newsroom. 6/10/2010.

13 - Boyden, E. S. and Chow, B. Y. (2010) "Defining An Algorithm For Inventing From Nature." Column, Technology Review. 1/19/2010.

12 - Boyden, E. S. (2009) “The Singularity and the Fixed Point.” Column, Technology Review. 9/4/2009. (http://www.technologyreview.com/biomedicine/23354/).

11 - Boyden, E. S. (2009) "Civilization as Experiment." Ed Boyden's Blog. Technology Review. 1/19/09. (http://www.technologyreview.com/blog/boyden/22512/).

10 - Boyden, E. S. (2008) "Averting Disasters, Preventing Problems." Ed Boyden's Blog. Technology Review. 9/2/08. (http://www.technologyreview.com/blog/boyden/22122/).

9 - Boyden, E. S. (2008) "Research as a Community-Building Activity." Ed Boyden's Blog. Technology Review. 7/28/08. (http://www.technologyreview.com/blog/boyden/22102/).

8 - Boyden, E. S. (2008) "Inverting the Core." Ed Boyden's Blog. Technology Review. 7/14/08. (http://www.technologyreview.com/blog/boyden/22096/).

7 - Boyden, E. S. (2008) "Training a Generation of Neuroengineers." Ed Boyden's Blog, Technology Review. 4/22/08. (http://www.technologyreview.com/blog/boyden/22055/).

6 - Boyden, E. S. (2007) "How to Think." Ed Boyden's Blog. Technology Review. 11/13/07. (http://www.technologyreview.com/blog/boyden/21925/).

5 - Boyden, E. S. (2007) "Synthetic Neurobiology." Ed Boyden's Blog. Technology Review. 10/9/07. (http://www.technologyreview.com/blog/boyden/21871/).

4 - Boyden, E. S. (2007) "Open Philanthropy." Ed Boyden's Blog. Technology Review. 9/24/07. (http://www.technologyreview.com/blog/boyden/21850/).

3 - Boyden, E. S. (2007) "In Pursuit of Human Augmentation." Ed Boyden's Blog. Technology Review. 9/17/07. (http://www.technologyreview.com/blog/boyden/21839/).

2 - Boyden, E. S. (2007) “Engineering the Brain (‘Notebooks’ column),” Technology Review, March/April 2007 issue, p. 34-35.

1 - Boyden, E. S. (2000) Computational and Theoretical Neuroscience: From Synapse to Circuitry. National Institutes of Health/National Institute of Neurological Disorders and Stroke, Technical Report for Workshop of April 28, 2000.

11 - GenBank: HM367071.1. Synthetic construct ArchT gene, complete cds. Submitted 5/27/2010.

10 - GenBank: HM367072.1. Synthetic construct ArchT-GFP gene, complete cds. Submitted 5/27/2010.

9 - GenBank: GU045594.1. Synthetic construct Arch-GFP gene, complete cds. Submitted 9/28/2009.

8 - GenBank: GU045595.1. Synthetic construct Mac gene, complete cds. Submitted 9/28/2009.

7 - GenBank: GU045593.1. Synthetic construct Arch gene, complete cds. Submitted 9/28/2009.

6 - GenBank: GU045596.1. Synthetic construct Mac-GFP gene, complete cds. Submitted 9/28/2009.

5 - GenBank: GU045597.1. Synthetic construct ss-Prl-Arch gene, complete cds. Submitted 9/28/2009.

4 - GenBank: GU045598.1. Synthetic construct ss-Arch-GFP-ER2 gene, complete cds. Submitted 9/28/2009.

3 - GenBank: GU045599.1. Synthetic construct ss-Prl-Arch-GFP gene, complete cds. Submitted 9/28/2009.

2 - GenBank: EF537649.1. Synthetic construct mammalian codon-optimized halorhodopsin gene, complete cds. Submitted 4/4/2007.

1 - GenBank: EU714030.1. Synthetic construct channel rhodopsin-2-GFP (ChR2-GFP) gene, complete cds. Submitted 5/11/2008.